| Module |
multicolvar |
| Description |
Usage |
| Calculate the components of the normals to the planes containing groups of three atoms. |
  |
Output components
This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.
| Name |
Type |
Keyword |
Description |
| lessthan |
scalar |
LESS_THAN |
the number of colvars that have a value less than a threshold |
| morethan |
scalar |
MORE_THAN |
the number of colvars that have a value more than a threshold |
| altmin |
scalar |
ALT_MIN |
the minimum value of the cv |
| min |
scalar |
MIN |
the minimum colvar |
| max |
scalar |
MAX |
the maximum colvar |
| between |
scalar |
BETWEEN |
the number of colvars that have a value that lies in a particular interval |
| highest |
scalar |
HIGHEST |
the largest of the colvars |
| lowest |
scalar |
LOWEST |
the smallest of the colvars |
| sum |
scalar |
SUM |
the sum of the colvars |
| mean |
scalar |
MEAN |
the mean of the colvars |
| _vmean |
scalar |
VMEAN |
the norm of the mean vector |
| _vsum |
scalar |
VSUM |
the norm of the mean vector |
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword |
Type |
Description |
| LOCATION |
atoms |
the location at which the CV is assumed to be in space |
Further details and examples
Calculate the components of the normals to the planes containing groups of three atoms.
An example input using this shortcut is shown below:
Click on the labels of the actions for more information on what each action computes
v3The PLANE action with label v3 calculates the following quantities:| Quantity | Type | Description |
| v3.x | vector | the x-component of the vector that is normal to the plane containing the atoms |
| v3.y | vector | the y-component of the vector that is normal to the plane containing the atoms |
| v3.z | vector | the z-component of the vector that is normal to the plane containing the atoms |
: PLANESCalculate the components of the normals to the planes containing groups of three atoms. This action is a shortcut. More details ...
ATOMS1the sets of atoms that you would like to calculate the planes for=9,10,11
ATOMS2the sets of atoms that you would like to calculate the planes for=89,90,91
ATOMS3the sets of atoms that you would like to calculate the planes for=473,474,475
ATOMS4the sets of atoms that you would like to calculate the planes for=1161,1162,1163
ATOMS5the sets of atoms that you would like to calculate the planes for=1521,1522,1523
ATOMS6the sets of atoms that you would like to calculate the planes for=1593,1594,1595
ATOMS7the sets of atoms that you would like to calculate the planes for=1601,1602,1603
ATOMS8the sets of atoms that you would like to calculate the planes for=2201,2202,2203
VMEAN calculate the norm of the mean vector
...
# v3: PLANES ...
v3_vatom1The CENTER_FAST action with label v3_vatom1 calculates the following quantities:| Quantity | Type | Description |
| v3_vatom1 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=9,10,11
v3_vatom2The CENTER_FAST action with label v3_vatom2 calculates the following quantities:| Quantity | Type | Description |
| v3_vatom2 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=89,90,91
v3_vatom3The CENTER_FAST action with label v3_vatom3 calculates the following quantities:| Quantity | Type | Description |
| v3_vatom3 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=473,474,475
v3_vatom4The CENTER_FAST action with label v3_vatom4 calculates the following quantities:| Quantity | Type | Description |
| v3_vatom4 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1161,1162,1163
v3_vatom5The CENTER_FAST action with label v3_vatom5 calculates the following quantities:| Quantity | Type | Description |
| v3_vatom5 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1521,1522,1523
v3_vatom6The CENTER_FAST action with label v3_vatom6 calculates the following quantities:| Quantity | Type | Description |
| v3_vatom6 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1593,1594,1595
v3_vatom7The CENTER_FAST action with label v3_vatom7 calculates the following quantities:| Quantity | Type | Description |
| v3_vatom7 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1601,1602,1603
v3_vatom8The CENTER_FAST action with label v3_vatom8 calculates the following quantities:| Quantity | Type | Description |
| v3_vatom8 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=2201,2202,2203
v3_grpThe GROUP action with label v3_grp calculates the following quantities:| Quantity | Type | Description |
| v3_grp | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=v3_vatom1,v3_vatom2,v3_vatom3,v3_vatom4,v3_vatom5,v3_vatom6,v3_vatom7,v3_vatom8
v3: PLANECalculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. More details ATOMS1the three or four atoms whose plane we are computing=9,10,11 ATOMS2the three or four atoms whose plane we are computing=89,90,91 ATOMS3the three or four atoms whose plane we are computing=473,474,475 ATOMS4the three or four atoms whose plane we are computing=1161,1162,1163 ATOMS5the three or four atoms whose plane we are computing=1521,1522,1523
v3_xsThe MEAN action with label v3_xs calculates the following quantities:| Quantity | Type | Description |
| v3_xs | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=v3.x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
v3_ysThe MEAN action with label v3_ys calculates the following quantities:| Quantity | Type | Description |
| v3_ys | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=v3.y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
v3_zsThe MEAN action with label v3_zs calculates the following quantities:| Quantity | Type | Description |
| v3_zs | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=v3.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
v3_vmean2The COMBINE action with label v3_vmean2 calculates the following quantities:| Quantity | Type | Description |
| v3_vmean2 | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=v3_xs,v3_ys,v3_zs POWERS the powers to which you are raising each of the arguments in your function=2,2,2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
v3_vmeanThe CUSTOM action with label v3_vmean calculates the following quantities:| Quantity | Type | Description |
| v3_vmean | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=v3_vmean2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=v3_vmean FILEthe name of the file on which to output these quantities=colvar
As you can see if you expand the shortcut above, the input calculates the vectors perpendicular to the planes containing
each group of three atoms. The mean value is then computed by adding all these three dimensional vectors together. The final
value output is the norm of this mean vector. This norm is large if the orientations of the planes containing the groups of
atoms are the same and small if they are not.
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword |
Type |
Default |
Description |
| LOCATION |
input |
none |
the location at which the CV is assumed to be in space |
| LESS_THAN |
optional |
not used |
calculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN. |
| MORE_THAN |
optional |
not used |
calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN. |
| ALT_MIN |
optional |
not used |
calculate the minimum value |
| MIN |
optional |
not used |
calculate the minimum value |
| MAX |
optional |
not used |
calculate the maximum value |
| BETWEEN |
optional |
not used |
calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN. |
| HIGHEST |
optional |
false |
this flag allows you to recover the highest of these variables |
| HISTOGRAM |
optional |
not used |
calculate a discretized histogram of the distribution of values |
| LOWEST |
optional |
false |
this flag allows you to recover the lowest of these variables |
| SUM |
optional |
false |
calculate the sum of all the quantities |
| MEAN |
optional |
false |
calculate the mean of all the quantities |
| ATOMS |
optional |
not used |
the sets of atoms that you would like to calculate the planes for |
| VMEAN |
optional |
false |
calculate the norm of the mean vector |
| VSUM |
optional |
false |
calculate the norm of the sum of all the vectors |
